One really minor thing I'd do differently: Rather than split on whitespace and then check length, just match 3 or more non-whitespace characters:

   #foreach my $word (split /\s+/, $line) {
   #    length($word) > 2 and $count_of{$word}++;
   #}

   $count_of{$_}++   for $line =~ /\S{3,}/g;
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